Musicians, chemists use sound to better understand science
The use of sonification to understand the physical mechanisms of protein folding led to a new discovery about the ways a protein can fold.

Date:
February 17, 2022
Source:
University of Illinois at Urbana-Champaign, News Bureau
Summary:
A team of researchers from music, chemistry and computer science
is using sound to better understand biochemical processes such as
the physical mechanisms of protein folding.



FULL STORY ========================================================================== Musicians are helping scientists analyze data, teach protein folding
and make new discoveries through sound.


==========================================================================
A team of researchers at the University of Illinois Urbana-Champaign
is using sonification -- the use of sound to convey information --
to depict biochemical processes and better understand how they happen.

Music professor and composer Stephen Andrew Taylor; chemistry professor
and biophysicist Martin Gruebele; and Illinois music and computer
science alumna, composer and software designer Carla Scaletti formed the Biophysics Sonification Group, which has been meeting weekly on Zoom
since the beginning of the pandemic. The group has experimented with
using sonification in Gruebele's research into the physical mechanisms
of protein folding, and its work recently allowed Gruebele to make a
new discovery about the ways a protein can fold.

Taylor's musical compositions have long been influenced by science, and
recent works represent scientific data and biological processes. Gruebele
also is a musician who built his own pipe organ that he plays and uses
to compose music.

The idea of working together on sonification struck a chord with them,
and they've been collaborating for several years. Through her company,
Symbolic Sound Corp., Scaletti develops a digital audio software and
hardware sound design system called Kyma that is used by many musicians
and researchers, including Taylor.

Scaletti created an animated visualization paired with sound that
illustrated a simplified protein-folding process, and Gruebele and Taylor
used it to introduce key concepts of the process to students and gauge
whether it helped with their understanding. They found that sonification complemented and reinforced the visualizations and that, even for experts,
it helped increase intuition for how proteins fold and misfold over
time. The Biophysics Sonification Group -- which also includes chemistry professor Taras Pogorelov, former chemistry graduate student (now alumna) Meredith Rickard, composer and pipe organist Franz Danksagmu"ller of
the Lu"beck Academy of Music in Germany, and Illinois electrical and
computer engineering alumnus Kurt Hebel of Symbolic Sound -- described
using sonification in teaching in the Journal of Chemical Education.

Gruebele and his research team use supercomputers to run simulations
of proteins folding into a specific structure, a process that relies
on a complex pattern of many interactions. The simulation reveals the
multiple pathways the proteins take as they fold, and also shows when
they misfold or get stuck in the wrong shape -- something thought to be
related to a number of diseases such as Alzheimer's and Parkinson's.



==========================================================================
The researchers use the simulation data to gain insight into the process.

Nearly all data analysis is done visually, Gruebele said, but massive
amounts of data generated by the computer simulations -- representing
hundreds of thousands of variables and millions of moments in time --
can be very difficult to visualize.

"In digital audio, everything is a stream of numbers, so actually it's
quite natural to take a stream of numbers and listen to it as if it's
a digital recording," Scaletti said. "You can hear things that you
wouldn't see if you looked at a list of numbers and you also wouldn't
see if you looked at an animation. There's so much going on that there
could be something that's hidden, but you could bring it out with sound."
For example, when the protein folds, it is surrounded by water molecules
that are critical to the process. Gruebele said he wants to know when
a water molecule touches and solvates a protein, but "there are 50,000
water molecules moving around, and only one or two are doing a critical
thing. It's impossible to see." However, if a splashy sound occurred
every time a water molecule touched a specific amino acid, that would
be easy to hear.

Taylor and Scaletti use various audio-mapping techniques to link aspects
of proteins to sound parameters such as pitch, timbre, loudness and
pan position.

For example, Taylor's work uses different pitches and instruments
to represent each unique amino acid, as well as their hydrophobic or hydrophilic qualities.

"I've been trying to draw on our instinctive responses to sound
as much as possible," Taylor said. "Beethoven said, 'The deeper the
stream, the deeper the tone.' We expect an elephant to make a low sound
because it's big, and we expect a sparrow to make a high sound because
it's small. Certain kinds of mappings are built into us. As much as
possible, we can take advantage of those and that helps to communicate
more effectively." The highly developed instincts of musicians help in creating the best tool to use sound to convey information, Taylor said.

"It's a new way of showing how music and sound can help us understand
the world. Musicians have an important role to play," he said. "It's
helped me become a better musician, in thinking about sound in different
ways and thinking how sound can link to the world in different ways,
even the world of the very small." Video: https://youtu.be/QdjJj7MGnGc ========================================================================== Story Source: Materials provided by University_of_Illinois_at_Urbana-Champaign,_News_Bureau.

Original written by Jodi Heckel. Note: Content may be edited for style
and length.


========================================================================== Journal Reference:
1. Carla Scaletti, Meredith M. Rickard, Kurt J. Hebel, Taras
V. Pogorelov,
Stephen A. Taylor, Martin Gruebele. Sonification-Enhanced Lattice
Model Animations for Teaching the Protein Folding Reaction. Journal
of Chemical Education, 2022; DOI: 10.1021/acs.jchemed.1c00857 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/02/220217131909.htm

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